Metamorphosis
by XxHeroxXxKillerxX
Summary: First Real Story! So take a peak inside and read it! 10-year old Naruto is brought through a change by a genetic monster from the distant past. A change that will carve a path of blood and gore through the ninja world and bring everything to an end. Naruto/Prototype Dark Naruto!
1. Introducing Change

I didn't understand it and I didn't think I could control it, yet. So I did the only thing I could. I waited. I waited for so long… and during all that waiting, I was fighting inside. Fighting to control the biological mayhem that was my genetic make up. I'm still not sure what I am but I am sure of who I am.

I am Alex Mercer and this is

Metamorphosis

* * *

Chapter One: Introducing Change

* * *

Naruto

"Remember class, stick to the shadows! Be as quite as you can, this is essential for your future survival as a ninja!" Tanezakura Kijiro, lead of Konoha academy class 3 droned on to his students.

"Yeah, yeah stealth and all that, Kijiro-sensei, why do we have to do this…" complained a loud and brash ten year old student.

"Well Naruto, if you want to live past twenty-" Kijiro stated, leaning to the boy in question. "- you'll stop being an _idiot_ and do the activity! Kijiro finished, smiling darkly as the other children around snickered at Naruto's plight.

Naruto was not phased in the least however, "Whatever Kijiro-sensei, nobody here can catch me anyways, I'm like a ghost."

"Say's the one whose afraid of ghosts…" A student named Sasuke deadpanned as the other children laughed uncontrollably at the boy.

Naruto now blushing and embarrassed beyond belief, turned away from Sasuke and waited for the exercise to begin. He would show them, in his own way.

About a minute later the class lead initiated the start of class by sound of whistle and the children to be ninja were off in a blur of motion.

* * *

Mercer

For a being that is supposed to be all powerful(at least to me) I sure had a terrible sense of time and direction. I was in a jungle of some sort, no immense skyscrapers, flying cars, nothing… in fact I don't even think I'm corporal at the moment.

What was I, vapor? Well that needed to change. I looked deep into my being, finding the individual particles of my being and if I had eyes at the moment they would have fallen out of their sockets.

My 'body' seemed to be scattered throughout the world, a world that I could feel was drastically different, even it's people. As that thought passed through me I got to wondering, my body was infinitely divided into particles, at a weight similar to that of the oxygen atom, so they would float in air. People could be _breathing_ me in!

I focused, and pulled at my 'body', and while doing this I could fell several large concentrations of, well me, in different parts of the world all packed into small areas. Near each of these concentrations were even larger areas where my particles seemed to rotate around. I tried tugging of the closest mass of my particles, it was also the biggest.

I found myself surprised as the particles would not rejoin me, startled and confused I willed myself to move towards the offending mass, forcing the free floating particles in the environment around me to bond to me, and eventually give me shape, longest three hours of my life

I chose to form into a familiar bird of prey, the hawk if I recall right and flew at a faster rate towards my objective.

* * *

Naruto

"_This is waaay to easy. I mean come on a stealth exercise? We should be learning some cool new jutsu or some thing_" Young Naruto thought as he hid from the chunin level ninja that were the proctors to the exercise he was in.

Naruto knew how to be stealthy, years of hiding from random drunken villagers has that effect. He had dug a hole in the ground and covered it up with a layer of grass he cut and rolled off over another layer of dirt, held up by a mesh shirt and several thick branches.

As he laid in his hole he let his thoughts wander, thinking of everything and anything with the exception of the one question he could never get answers to. Thoughts of passing the academy and becoming a ninja, saving princesses, nations, and even the whole world! He thought of the only person to acknowledge him, Hiruzen Sarutobi, the Third Hokage, his Jiji. He almost laughed in glee when he thought of finally becoming the next Hokage, then having a big family… then he'd make sure…

He was pulled from his thoughts as a man landed directly above him, the man looked around confusedly for a few seconds. Before dropping to his knee and fingered the ground.

Naruto held his breath and willed himself to be as silent as possible as he listened for the man to leave.

" I was sure…" The man began to mutter but was interrupted by another man jumping down beside him.

At this point Naruto was worried if his quickly made hole would hold up, which would have sucked 'cause he just finished it.

"Iruka-senpai, what are you doing here? We still have about 35 students to find." By the voice Naruto guessed it was Kijiro-sensei.

"I had felt a student around here with my ability…" The man now identified as Iruka said.

"And, where are they… nothing can get pass your Kekkei Genkai."

"Well, that's the problem, the signature I was tracking went cold. Like it was never there in the first place."

"Well Iruka-senpai, seems your days out of ANBU have made you rusty" Kijiro laughed out.

"Kijiro?" Iruka called out

"Yea, what?"

"Fuck you." Iruka said as he jumped away from the clearing. Kijiro chuckled again as he jumped away after him.

Naruto, after he was sure the two were gone released his breath and relaxed before smirking to himself. '_I. Am. Freaking. AWESOME!_' Was all he could think to himself.

A couple of hours had passed into the test and Naruto was just about to fall asleep in the little hole he had dug when he first felt it. A little pull at first but as the minutes went by the feeling got stronger and stronger.

"_What the… hell… is this!_" Naruto thought in agony as he blacked out. All alone in the forest in a hole he had dug, where no ninja would look. And as the hours passed on Naruto's stealth skills were no longer in question.

The lead of class 3, Tanezakura Kijiro and the lead of class 4, the man by the name of Umino Iruka whose class had joined in on the activity had called for the village ANBU to find the boy.

They may not have liked the boy, but the container of the worlds most fearsome demon being captured by a rivaling nation was a security risk few would wish to take.

* * *

Mercer

I tracked down my particles to a small patch a forest inside of a small city, the city itself I couldn't speak for, there was hardly any technology, there were no skyscrapers to speak for and the only impressive things were four faces carved into a mountainside that reminded me of something similar from my past. Couldn't recall what though.

As I flew closer and closer to the conjunction of particles, identifiable mine I felt a pull, a weak pull that I could have ignored. But as intrigued as I was I gave myself to the feeling. I mentally cringed as I felt my current form be ripped apart, forcing me into my particle/vapor form.

Had I been a lesser being and unable to focus through unimaginable pain, I would have surely blacked out. Fortunately, I am not a lesser being, and my awareness stayed intact through the harrowing experience.

I felt myself being forced through what felt like an incredibly narrow space, twisting and contorting me any and in every manner. My form churned in this funnel-like spiral at every angle possible at the highest speeds imaginable. However, at the same time I felt as if this event had taken place over the span of a few decades. In retrospect, I realize it had only transpired in a matter of seconds.

Just as quickly as it had begun, this rollercoaster from hell chose to abruptly end. It felt as if the combined mass of two stars had crashed into me at once. And as I thought this I calculated just how large of a mass and the force that would inflict upon me. If I could laugh, I would've. Two average sized stars have a combined mass of 100 or so solar masses and at the speed I _think_ I was moving at… I may as well be immortal.

But I knew better, I may be damn near indestructible and have a potential life span double that of your average neuron star, but everything dies eventually. The same goes for me, whether it be by another's hand or old age, it'll happen.

A fact made painfully obvious by my blacking out for several moments…

* * *

Training Ground 87 - Forest of the Child

The night sky was beginning to consume the sky as several figures stood silently awaiting further orders from their leader, The Sandaime Hokage, Hiruzen Sarutobi.

The wizened Kage eyes hardened at his subordinates as he took in what the ex-Anbu captain, now academy teacher reported to him.

The stock still chunin were taken aback by the sudden coldness in their beloved Kage's warm brown/grey eyes. Even more so when they heard his voice.

"So, not only did you fools lose Naruto, our resident Jinchuruki. You've also failed to find the Uchiha. Who might I add is the last _loyal_ Uchiha alive." The angered Kage all but seethed out.

Umino Iruka stepped forward and kneeled before the man, head bowed deeply before speaking up.

"Hokage-sama, please forgive my subordinates for their… lackluster performance tonight. The issue with the Uchiha brat has already been resolved, a kage-bunshin of mine has traced the boys heat signature at his home, asleep in his bed." Iruka said respectfully.

"And pray tell, Iruka-kun, was he at his home instead of the Academy." The Kage ordered.

"When questioned of his absence, the boy informed me that a sensei here dismissed him from the remainder of the training camp." Iruka informed.

"And which instructor gave this order?"

"Orosume-san, Hokage-sama."

"I did no such thing!" Misa Orosume; a pale faced chunin with dark brown shoulder-length hair and light green eyes; roared in rage, earning the glare of the Sandaime for her interruption.

Misa froze in place as the old man raised his eyes to meet hers, all her senses screaming at her to run but her body would not move. Such was the extent of her fear of the elderly Kage.

The Kage turned his gaze back to the man kneeling in front of him and gave a whole hearted laugh as if amused by the whole situation before resting his hands upon Iruka's shoulders.

"Iruka-kun, your Dakajigan [Fire Catcher Eye ] has again and again proven its inert worth in Konoha's forces. It pains me to this day that your family had to have perished in the Battle of Kyubi." The Kage said with a small smirk.

"Hai, Hokage-sama."

"Rise, Iruka-kun, rise," the Kage started as Iruka stood. "Now my dear boy," Hiruzen leaned closer to Iruka as if to whisper in his ear and yet spoke loudly enough that all in the clearing could hear him speak.

"You know what we do to ninja who fail to follow orders… don't you Iruka-kun." The Kage didn't ask Iruka as much as he ordered him, and from the stiffening of Iruka's shoulders and the strain in his voice, he knew as well.

Misa, in all her fear could do little to speak her case, she knew she hadn't done the deed. She presumed Iruka knew as well, so it came to set in her mind that the Kage knew she had done no wrong, and would still…

"…Yes, Hokage-sama…" Iruka managed through clenched teeth that threatened to chip one another once the Kage tightened his grip on the man.

"Is that _hesitance _I hear… _Iruka._" The Kage said in a almost singsong manner, his voice having no trace of the coldness before. Only the warmth of a grandfathers voice.

Iruka knew better however, as apparent by his body stiffing even more under the Kage's grip.

"No, Hokage-sama, it is not." He replied

"Then _what _is it? " The man asked

"Anticipation sir," Iruka grounded out.

"Good, now you have my orders"

"Hai."

The Kage released his grip on the ex-ANBU who immediately spun around and, faster than the human eye, charged forward and ran his arm through Orosume Misa's chest before she could utter a word.

The man stood there for a moment with Misa, slouched on his arm, a arm which was on fire.

"You see Orosume," The Kage began, spreading his arms wide for emphasis, "Whether or not you actually dismissed our young Uchiha from the exercise matters little in my eyes, in the eyes of Konoha. What does matter is that a message is conveyed to the people whose best interests would be to heed it."

Misa, through half lidded eyes and a blood filled mouth, managed to ask the question all shinobi present had on their minds.

"And…that would be…Hokage-_sama_" she ground out, not hiding the hate in her voice.

The Kage smirked before continuing his explanation

"That Konoha is not at all weak…Konoha and by extension, me, are not to be messed with."

The dying shinobi's eyes widened at his words before coughs wracked her body, blood splattering onto Iruka's face as she died on his arm. Iruka, who had long ago deactivated his _Kekkei Genkai _ability let the heated corpse fall from his arm in a gruesome display, leaving charred chunks of flesh on his blackened arm.

"You better find Naruto-kun too, Iruka-kun. We wouldn't want more blood spilt at your hands would we." The Hokage said in Iruka's ear before using shunshin to disappear from sight.

The ninja all stood there, most staring at Iruka in barely concealed pity or staring at Misa's smoldering corpse slowly turning to ash before their eyes. Iruka's gaze however remained on his arm. An arm blacked by Misa's burned blood and flesh, an arm blackened by sin, a sin so incorrigibly it haunted him to this day.

Despite all this Iruka ordered the remaining chunin.

"Find him…"

* * *

Mercer

As I regained consciousness I was instantly aware of the fact that I was in my human form. As I gazed upon my naked form I noticed red steaks running across my left fist and blue across my right. Chalking the oddity up to having to do with what happened to me earlier. Concentrating, I altered the molecules of my skin to change appearance and shape. My new apparel was something I felt more suited for. I now appeared to be in a pair of black slacks with white lining at the creases. Above it I wore a white muscle shirt covered by a dark grey dress shirt that was open at the top. I chose not to alter my feet because it appeared I was ankle deep in murky water.

After staring into the immeasurable darkness for a minute or so I started treading my way deep into the inky darkness. As I advanced the area around me lit up in array of colors causing me to pause. As soon as I stopped the colors seemed to retreat back into the darkness as if urging me to continue walking.

I complied and continued walking into the now illuminated darkness, watching as the rainbow of colors twisted and morphed before my eyes. The moment would have been beautiful if not for the oppressive yet familiar aura emanating from deeper in the darkness. So I pressed forward, ignoring the colors and focusing on the aura. Eventually I found myself in front of a large broken gate. The colors from earlier raised in anticipation over the hole in the gate, shimmering and pulsating as if it was alive.

Inspecting my surroundings, I saw that closer to the gate there was a raised alter wrapped in gold cloth with red trimmings. There was something laying on top of the alter that, from my distance, I couldn't readily make out. I walked to the alter, morphing my feet to look as if I was wearing a pair of black high top sneakers that I remembered from my human life to accommodate to the hard concrete like floor.

On the alter was a boy, barely 11 years old, wrapped in more of that gold cloth, that upon further inspection was made of silk. The boy was pale, incredibly so. I checked the boy for a pulse and frowned when I didn't feel one. As I removed my hand a whisper of white light circled around the boy franticly. More and more of these white lights circled him until a loud growl was heard past the cage, causing the whole area to shudder. The wisps scattered back to the darkness before circling around each other for a few seconds. Then in a burst of speed the lights shoot over towards the barrier of colors.

I narrowed my eyes as I felt the malicious aura approach the gate at a rapid speed before crashing into said barrier. My eyes widened despite myself at the massive creature that was before me. A massive nine tailed fox had crashed into the equally huge black gate and destroyed it with not a scratch on itself, only to be stopped by the barrier of light which blew the giant fox back on its backside. The beast roared in aggravation, shaking the area violently.

The beast got sat on its hind legs, tails sweeping around violently before taking in the guests in its prison.

I saw the beasts crimson eyes widen in shock before it got to all fours and sauntered back in front of the gate, tails swishing happily in the air.

I was further shocked by the beast opening its maw and speaking to me.

"**Master! You… you've returned! Are you here to free me from this lowly human!**" The beast spoke.

I decided to go about this calmly, to figure out who exactly this beast thought I was.

"Who and what are you creature?" I spoke out to the fox.

"**Master! It is you! Free me now I ask of you!**" The fox said hurriedly, rambling on about its master returning.

At this point I was annoyed at the being basically ignoring me so I voiced it.

"Silence beast!" I shouted out. "What are you creature!"

The fox looked at me confusedly before speaking out. "**But Master, you are me and I am you. Aren't you here to absorb me into your being once more? Its been centuries since you split us up protect you from the humans and their weapons!**"

I looked at the being confusedly before recognition crossed my face. The fox noticed this too if the widening of its eyes was anything to go by.

"**Master! No!**" The fox roared out.

I was about to wonder why before a sharp pain in my head brought me to my knees. I gasped as memories crossed my vision. I could scarcely hear the fox banging against the color barrier trying to get to me as I blacked out once more.

* * *

_End of Chapter One_

* * *

Alright that's the end of this chapter of Metamorphosis. I hope you guys like this new story I am writing and hope that you will comment and review. This will be my first real story, and I'm not planning on giving up on it. As you've read, it's a Naruto-Prototype cross and believe me, its nothing like you've read before so stick with me guys. I want at least 15 reviews for the first chapter! So do your jobs readers and review!

On a more serious note I'll have polls open for some major/minor decisions throughout the story! I might do a pairing poll as I haven't decided which female character will work for the Naruto I'm trying to build as well as work for the Konoha I'm trying to build. As you can see Hiruzen is a much different Kage in this fiction than in others. I gave him the ruthlessness of Onoki and the cunning of Danzo add to that his own abilities of manipulation and the fact that he's stronger than both those individuals I believe I've made a great tyrant out of Hiruzen. Just wait until you figure out why.

Alright I'm XxHeroxXxKillerxX and this is sayonara!


	2. Thus It Hath Begun

_OI! I don't own Naruto or Prototype!_

* * *

_Previously on Metamorphosis _

_The fox looked at me confusedly before speaking out. "__**But Master, you are me and I am you. Aren't you here to absorb me into your being once more? Its been centuries since you split us up protect you from the humans and their weapons!**__"_

_I looked at the being confusedly before recognition crossed my face. The fox noticed this too if the widening of its eyes was anything to go by._

"_**Master! No!**__" The fox roared out._

_I was about to wonder why before a sharp pain in my head brought me to my knees. I gasped as memories crossed my vision. I could scarcely hear the fox banging against the color barrier trying to get to me as I blacked out once more._

* * *

Chapter Two: Thus It Hath Begun.

* * *

Mercer: 5,000 Years in the Past

I gasped as I opened my strained eyes, trying desperately to focus my vision enough to recognize my surroundings. Eventually my blood-shot eyes focused and the pounding in my head ceased, only for but a moment however. As soon as I recognized where I was my migraine exploded throughout my head once more. I staggered as this happened, clutching the sides of my head gingerly. I stumbled about until my migraine ceased once more and tried to focus my self.

"Okay, either I just dreamed everything, or I'm in the past again" I heard my self mutter as I looked around the cream colored walls of the small two bedroom apartment I found myself in.

It was my old home… when I was human, before I turned into what I am today. I closed my eyes and prayed to whatever gods there were and checked to see if my genetic morphing abilities were _actually_ real. I thought of changing my right arm into a claw.

"…"

I opened my eyes and true enough my arm way a warped metallic claw which shuddered and tensed in anticipation. I sighed and allowed my arm to revert back to its normal form. I walked to the exit of the apartment, scowling deeply, and opened the door.

I was immediately blinded by the bright light and had to stop my self from stepping outside the room. To my shock and confusion there was no dark hallway for my feet to step, only a vast sky filled with clouds. I peered down past my feet towards the earth below and frowned at what I saw.

Below me was a huge mushroom cloud rising over an ocean. I instantly recognized what it was. The atomic bomb that Black Watch soldiers threatened New York city with, the bomb I saved New York from. It struck no small chord within my self to realize that this was when my memories of the past became jumbled and confused to the point of being undecipherable.

_Quite right Alexander, this is the last event you remember personally. Your heroic action of saving the colossal city behind us._

I swirled to my right as I heard the sudden voice, my arms automatically changing into metallic bladed weapons of destruction. My right arm featured my claw while my left morphed into a single large scythe blade.

"Whose there!" I shouted in alarm as I swiveled my head left to right.

_We are one of the guardians of the boy you now find yourself imprisoned within._

_You can call us Akina, creator. _

I relaxed as the apparition appeared before me, reverting my arms to normal as I did so. I chose to examine the woman instead of voicing my immediate questions. She was a light skinned woman and a tall one at that. She stood at six feet with long velvet blue hair draped down her back, curling outwards at the base. Her eyes were very narrowed, but not to the extent you thought she was glaring at you and were a calm light brown color. The rest of her figure was hard to make out as it shifted and warped constantly. Only her face was clear and without shimmer.

"Explain," I practically demanded "The guardian part." I continued after seeing her questioning gaze.

_As we said, we are one of the guardians of the boy whose mindscape now imprisons you, creator. _

"How am I imprisoned, and are you speaking of the dead boy I saw on that alter?" I asked, ignoring her odd speech pattern.

_Yes, and said boy's name is Uzumaki Naruto. To explain your imprisonment would be to explain how we and by extension, the energy source chakra, came into existence._

"Then tell me… Akina"

The apparition smiled at me before speaking.

_That we cannot explain to you Alexander, it has been… forbidden to tell you when you are not ready for the truth. And it has yet been deduced that your mental state is ready for such a truth. we can, however explain to you the boy and of the prophecy that surrounds him. As well as the creature that dwells inside of him._

I frowned at the woman as she said this, only inclining her to smile more. I decided to play whatever game she was playing.

"Then explain that then…"

_Gladly, ten years ago a man by the name of Minato Namikaze battled the massive fox that was in the cage you saw. He could not defeat the fox so he sealed the fox into a newborn baby, his son, Naruto, killing himself in the process, leaving the boy with out parents, seeing as his mother died giving birth to the boy due to… complicated circumstances._

"…And what of the prophecy you speak of?"

_Two thousand years ago two prophecies appeared to us. One spoke of the birth of the ninja as the people of this era know it. The other spoke of a boy, tainted by the Darkness and touched by the Light come to end the age of the ninja and resurrect the true age of man and bring a definite peace back to humanity. We have made certain that this boy is the boy of prophecy._

I narrowed my eyes at that "And what means do you speak of?"

The being seem to giggle before throwing its head back in laughter. I tensed as the being started glowing white as it opened its mouth to speak to me.

_Means! _Another fit of laughter. _We ARE the means! We are everything, anything, and nothing at the same time! We ARE chakra! _

_Perhaps if we told you how to regain your memories of the past you shall be sated… _The being seemed to be in conflict with itself before continuing.

_Go forward mortal! Leap into the event below you and a fragment of your past shall be revealed to you yet!. _The being all but shouted before vanishing, leaving me to stare at the still pluming mushroom cloud as I contemplated its words.

I shrugged my shoulders before I jumped out the floating apartment, not noticing it disappearing the moment I leaped or smiling figures floating behind me as I fell headlong into an otherwise assertive demise.

My only thought as I fell into the mushroom cloud of superheated oxygen and water molecules was not surprisingly the very topic the being avoided.

'_What the hell is chakra!_'

* * *

Konoha - Kage Tower - Kage's Office

Sarutobi Hiruzen let a wicked smile grace his face as he sat in his worn chair. He chuckled to himself as he pulled his wooden pipe out from his upper-left most drawer.

As he began filling it with tobacco a series of knocks rapped on his office door. He recognized it immediately as his long time partner and best friend, if you could call 50 years of crossing one another a friendship at least.

"Enter Danzo-kun." The Kage said loud enough to be heard across the wide room and almost immediately Danzo entered the office.

Danzo slowly hobbled his way over to the plush antique chair in front of Sarutobi's desk, speaking as he did so. "Glad to see that you are well Hiruzen-dono."

"Likewise Danzo-kun," The Kage started while smiling softly. "What brings you to an old mans office at this time of night, surely it cannot be for the pleasure of my company."

Danzo replied, hiding his slight sneer at the Kage's intuitiveness. "Right as ever Hiruzen-dono."

Sarutobi smirked before speaking again. "I assume you've become aware of the _proceedings _outside of the Shirin no Warabe."

"Indeed, ironic how you lost several students in a forest renowned for being safe." Danzo replied with the ghost of a smirk.

"I'm afraid it isn't just a mere child that got themselves lost Danzo-kun." Sarutobi baited deceptively.

"Of course not Hokage-dono, but its always the forgotten kunai that cuts you." Danzo replied nearly grinning despite himself.

Sarutobi nearly laughed as his rival fell for his trap.

"You of all people should know that Danzo-kun, with your recent tryst with the Daimyo of Kaze no Kuni nearly being interrupted by a few rouge assets of yours." Hiruzen said, his smirk broadening as he watched his rivals triumphant look crumble into one of cold disgust.

"Believe me when I say those assets were frozen Hokage-dono." Danzo replied, his tone obviously colder than before. Hiruzen however, was not deterred from angering is life long rival in the least.

"Danzo-kun, if you insist on continuing to siphoning funds from Sunagakure through exchanges with their Daimyo, make sure none of your _broken_ _toys_ find someone else to _play_ with them." Sarutobi baited again.

Danzo scowled before replying with his own insult. "Better to have broken toys than _tortured _toys. My men respect and honor me, yours only fear you Hokage-dono." Danzo said angrily as he stalked to the door leading out of the office.

"And there is where we will always differ my old friend, ruling through fear is so much more _appeasing _than through other means." Sarutobi said in an almost gleeful tone as Danzo left his office.

Danzo felt a shiver run through his spine as closed the door behind him, hearing the faint cackling of his life long friend.

'_Or what's left of him at least…_' Danzo thought as the insane cackling grew louder.

* * *

Konoha: Shirin no Warabe: Sector 5

"Iruka-senpai, why are we back here, we cleared this sector hours ago." Tanezakura Kijiro asked his ex-ANBU commander superior.

"Kijiro, do you know the only way someone can hide from my Kekkei Genkai?" Iruka asked of the man to his right as they walked into a wide clearing.

"No, no I don't know. Where are you going with this." Kijiro responded.

"There's two ways, the person suddenly dies or they go underground. Which do you think is more likely for our wayward student." Iruka said as he walked over to the exact spot he stood over hours earlier.

"You mean he's under there?"

"Positive." Iruka answered as he pulled out a kunai and as he was about to start checking for loose soil a massive surge of chakra caused him and Kijiro to freeze.

"What…the…hell…" Kijiro struggled out as the chakra oppressed the two.

Iruka had to _actually_ strain himself to crane his head to Kijiro's direction.

'_Such power!_' Iruka thought to himself, rooted to the spot as he was.

"…R…Run!" Iruka ground out to his fellow sensei.

"Wh…what?" Kijiro replied shocked.

"RUN Kijiro! NOW!" Iruka forced out as he was dragged to a knee by the oppressive power.

However it was little too late for Kijiro to escape, they both felt a massive pull from the earth below them in the hidden boy's direction before a bright flash of light blinded the two.

* * *

Mercer: 5,000 Years in the Past

I had expected searing heat and intense air currents as I fell through the cloud of super heated water and oxygen particles but was mildly surprised that all I felt was a gentle breeze and a slight warming sensation in my face and hands. I contemplated this as my decent slowed to a halt by some unknown force and deduced it was probably because this was all a forgotten memory.

Underneath me a pure white platform materialized and the force holding me let go. I landed gently upon the grid like platform and peered further down. Instead of seeing a bubbling ocean and steam from the evaporated H2O particles like I expected, I saw a large black metallic orb covered in pulsating red organic material. I recognized it immediately as a form of my Critical Mass transformations. I've never used this form of mutation however and was genuinely intrigued when as soon as I thought of how to do it again, memories of the event ripped through my subconsciousness. I nearly fell to my knees as it happened, but I remained strong as my legs wobbled and my hands rubbed against either side of my temples in a vain attempt to alleviate the pain.

'_Looks like regaining memories is still as painful as ever… great._' I thought to myself as I watched the pre-experienced event transpire before me. '_I could never hope to get out of the blast range unscathed, so I did the next best thing. Absorbing the mass of several thousand gallons of ocean water and creating a defense as impenetrable as possible. Looks like it worked, but not without its consequences it seems. Absorbing and expelling all that mass so quickly had left me comatose for a few days, giving Blackwatch ample time to attack me once more in retaliation._' I replayed the events in my mind as they developed below me, seemingly in time with my mental narration.

I watched as bomb after bomb struck the still floating dome of my creation, not one leaving a dent or even a scratch. Not even several nuclear bombs could pierce the estranged orb and soon Blackwatch relented their attacks, probably figuring that the wide scale of radiation that I've had to have been exposed to would kill me. They were right to an extent, it did '_kill_' me, pushing my coherent mind deeper and deeper into my psyche as my body struggled to adapt and mutate in order to compensate to the loss of mass from the Critical Mass transformation and the radiation.

'_And that's when it started… mother…_' I thought as the world around me faded into a deep inky blackness, my understanding of my situation grew as the confusion in my mind relented to realization. I had a theory that needed testing, however I needed to speak with the estranged fox in that boy, Naruto's mindscape.

I chuckled as I thought of the upcoming days, they would surely be amusing to say the least.

* * *

_End of Chapter Two_

* * *

Alright! End of the second chapter! As you can see its fairly short, only being about 2,500 words without the AN. However, this being one of the intro chapters leading into the story I feel its justified. And the fact I wanted to give you guys a little cliffhanger for you to grip the ends of your chairs with.

I would personally like to thank Joseph-Alexander, Forgottenkami, and puma1sunfire for taking time to review the story, ConnectFire611 for adding me to his C2 ConnectFire611's Favorites and the 197 other people who read the first chapter in the few days its been out. Thanks guys!

So Review and tell me what you think of the sentient Akina and her creepy speech pattern and please! Tell me whether or not I make Alex a little too OC than he should be, I haven't played the second game ye so I don't know his behavior to the dot there. Worry not however! Prototype 2 will be included in this story! I've read and watched enough of the game to know what Alex does to Heller and that Heller kills him, so just wait and see how I integrate this with the story.

Ight This Was XxHeroxXxKillerxX and this is sayonara!


	3. Alpha and Omega

_Previously on Metamorphosis_

_I watched as bomb after bomb struck the still floating dome of my creation, not one leaving a dent or even a scratch. Not even several nuclear bombs could pierce the estranged orb and soon Blackwatch relented their attacks, probably figuring that the wide scale of radiation that I've had to have been exposed to would kill me. They were right to an extent, it did 'kill' me, pushing my coherent mind deeper and deeper into my psyche as my body struggled to adapt and mutate in order to compensate to the loss of mass from the Critical Mass transformation and the radiation. _

'_And that's when it started… mother…' I thought as the world around me faded into a deep inky blackness, my understanding of my situation grew as the confusion in my mind relented to realization. I had a theory that needed testing, however I needed to speak with the estranged fox in that boy, Naruto's mindscape._

_I chuckled as I thought of the upcoming days, they would surely be amusing to say the least._

* * *

Chapter Three: Alpha and Omega

* * *

Mercer: Naruto's Mindscape: 1 Hour from the Present

I groaned as I picked myself out of the murky waters that held no warmth and no cold, watching with half-lidded eyes as the drops of darkened water fell off of me as if I was never there in the first place, leaving me completely dry.

"**So you've reawakened Master, that is good." **I heard as I began to take in my surroundings, narrowing my eyes as I recalled the… dream, vision or whatever it was that had happened to me.

"Fox…" I started, trying to find the right way to approach the situation before the fox spoke once more.

"**I am known by my brethren as Kurama, master."** The fox stated. I looked at the massive fox oddly, pondering on it's change in demeanor before the fox once again spoke up.

"**Your presence here has served to… significantly calm my rage filled mind, leaving me coherent enough to regain fragments of my chosen personality. Fragments which have been lost for countless ages without your stabilizing effects, Master. " **I nodded my head as I listened to the Fox's, no, Kurama's explanation.

It made sense, I made this creature, unknowingly or not, so it's not surprising that my mind stabilized his.

"There are more of your kind, aren't there Kurama?" I asked the fox, getting straight to business. The fox nodded before it spoke, its deep, hollow, voice reverberating through the sewer like mindscape.

"**Yes there are nine others, eight of which are sealed into other human children, at least that's what our senses are telling me." **I nodded my head in acknowledgement, that explains how I found this boy in the first place.

"What of the last? When I searched earlier, I sensed only nine, including you." I asked of Kurama, recalling the moments after my awakening where I search for the scattered particles of my form.

"…**I have not been able to sense the last of us for at least three millennia." **Kurama replied, his head bowed in shame.

"**Forgive me master, as the leader of the original nine I should have done better to-"** Kurama apologized, however I could not hear the words that I felt shaking the mindscape.

"Kurama," I interrupted him. "Do not waste your breath," At this the foxes head bowed low to the ground and his tails swiped the air with fear. "Something is blocking whatever it is you intend to tell me from my senses." I explained to Kurama, his face curling into a snarl as he growled, his tails lashing angrily against the chakra barrier.

"**It's those meddling beings!"** Kurama roared in anger before he started speaking to me once again. It was for naught however because every word that left his mouth I could not hear and because he was a fox I could not read his lips.

"Stop, they're doing it again." I said loud enough for Kurama to hear me. He snarled again as red energy poured from behind him and struck the glowing wall of ever-changing colors. The violent energy felt to me as my own hands, familiar and appreciated, I gazed towards the barrier that surged brightly with energy as Kurama attacked him. I sent my will towards the lashing energy and immediately the power halted and surged back to Kurama.

"This is unnecessary Kurama, it seems whatever these creatures may be, they're strong enough to hold me here. That should be enough to tell you your attempts to break through them would fail." I spoke to the fox before continuing "Since it seems getting out of here is not an option and that getting further information of the situation from you is not going to happen we will have to rely on this boy." I spoke as realization raced across Kurama's crimson eyes.

"**You plan to do **_**that?**_" Kurama questioned, his vulpine eyes widening.

"It's the only way… besides, I think me coming into his body has killed him, it's the least I can do…" I said while walking back to the alter where the boy, Naruto, laid his form unmoving and cold. I trailed my hand over the thin golden colored silk cloth that covered his face. I pulled the cloth from his pale almost blue face and frowned.

"Kurama, how's this boys life been?" I asked to my other self.

"…**I am not sure, I know it has not been the best being that is the fate of all Jinchuruki but this seal doesn't allow me to tamper with the boys mind let alone see his memories.**" Kurama answered.

I sighed deeply before looking into Kurama's crimson eyes. "Well lets get this show on the road eh?"

"**You do know what this will lead to Master…**"

"It's the only way.."

"**You don't have too! He's just one human!**" Kurama protested

"One human… heh, Kurama, remember we were human once…" I replied, causing the massive fox's eyes to widen.

"… **Okay… do it Master…**"

"Gladly…" I muttered before slamming my out-stretched hand into Naruto's chest. I was not surprised when my hand instantly sank into him. Nor was I surprised by the streams of bright red organic material that pierced through the golden cloth and into my arm, pulling me farther into the boy. I watched as the color returned to his face and his eyes burst open as my arm sunk deeper into him.

I watched as panic rushed through his bright ocean blue eyes as he looked into my own light green eyes. Neither of us could speak, on the account of the unbelievable pain and the shock respectively. I found that words were not needed however, as each second more of my body was absorbed into his and each second more of my memories became his. We were bonding. Becoming something more than either of us was alone. He was Alpha and I Omega, the beginning and the end…

* * *

Konoha: Shirin no Warabe: Sector 5 - Iruka

* * *

I struggled in vein as the pressure drew my college and me closer to its origin point, the spot I believed Naruto to be. What this power could be, I thought. I knew it was not the vile kitsune's chakra; this was too… cold for that.

I recalled the night 10 years ago when I had lost my family to the creature. Its power was maddening, nearly suffocating me in its wrath as it destroyed nearly every city in the countryside of Hi no Kuni or fire country. As the massive creature made it's was to Konoha's main gate its terrifying chakra swept across the village in waves, scorching anything remotely combustible. Its initial attack alone gave severe burns to hundreds of ninja, most of which were located _miles_ within the city. God knows what became of the few dozen that were stationed on the walls.

Soon after that the Third had taken me in, raised me like a son. Even then, I found his actions suspect. Why take me on when there was an ostracized baby that needed the attention more than I did? It was only later I had found out that the Third had trained me in secret, no one knew, no one cared. I was just another orphan. I tried to make myself believe that it was the loss of his son and wife that night which prevented him from publicly coming out with it.

I loved him… as a father and I realized that he did not care for me… just for my Kekkei Genkai.

Now… I hate him, I despise him and everything he stands for, even more so than the monstrous being called the Kyuubi no Kitsune.

In any case, this was not that, this was… something ancient, older than the Kyuubi, something raw.

The pressure increased to the point I was having trouble remaining conscious, through it all I glanced over to Kijiro, the man was unconscious, his body being pulled across the ground toward me. I could only stare as his body smashed into mine, crumbling the last of my chakra- powered resistances as my back landed on the dirt floor below me.

I felt the ground give, causing a patch of earth below my upper back and head to fall into the hollow hole below. I could do nothing as my head fell inside of the hole. What I saw could only be described as shocking.

It was Naruto, the boy who most of the villagers have come to associate with being its pariah. His face was pale, incredibly so, I felt out with my Kekkei Genkai and had to stifle a gasp when I felt absolutely _nothing_. Naruto was for all intents and purposes, _dead_, and judging by just how _cold_ he was it's been at least nine hours. The start of this joint exercise was six hours ago... This made no sense to me. He should not be so cold this soon if he was truly dead!

Nevertheless, if he was dead why was this crippling pressure coming from him?

I had little time to ponder the matter as Naruto's body to my utmost horror began shaking violently. I could hear his bones snap in protest of the sudden movement. A sign of Rigormortis in its third stage.

Rigormortis is the rigid stiffening of the skeletal structure and muscular structure shortly after death. It has four noteworthy phases that could be used to determine time of death. If a body was warm and flaccid, the body has been dead for less than three hours. If the body was warm and stiff, the body was dead for at least three to eight hours. If the body was cold and stiff, the body has been dead for more than eight to 36 hours. In addition, if the body was cold and flaccid then you assumed the body has been dead for longer than 36 hours.

My eyes widened in morbid fascination as I watched his snapped and shattered bones pierce his flesh at odd and disturbing angles, shooting small but thick streams of dark coagulated blood from them.

I felt myself sighing in relief when his body soon stopped convulsing and the insane pressure disappeared. I closed my eyes and slowly began to shift Kijiro off my person and rolled over onto my hands and knees before I felt it. A heat, more intense than anything I have ever felt before in my life erupted below me. My eyes shot open and glowed the bright orange that easily identified me as a Dakajigan user and focused on the boy below.

His form was writhing, hands clutching at his head in a clawing manner, his eyes were open and widened, and his pupils were so dilated you could barely see the cerulean color of his irises. His mouth was opened in a silent scream of agony as his bones that were previously sticking out of him were violently pulled back in and snapped in place, leaving the wholes from whence they came to close up rapidly.

All of this happened in the span of a few scant seconds before it ended as quickly as it had begun. His body stilled and chilled to its previous temperature in an instant. Before I could do anything to check on the boy or as my instinct told me, to escape, a guttural scream escaped Naruto's mouth. He was howling in a bestial manner that for a moment I believed the Kyubi that he contained had escaped.

I stood up, shaking at the effort. The aura from before must have damaged my body somehow. I pulled Kijiro onto my shoulders in a firefighter carry, grunting at the effort. I channeled chakra throughout my body to strengthen it and leapt away. I had to escape! Whatever was happening to Naruto below I did not want to stick around and watch.

Before I could get more than several meters up to the nearest tree branch, I felt something latch onto my ankles and give a vicious tug.

"Shit!" I yelled out in shock as my body collided with the; thankfully; solid ground below. Landing in that pit Naruto dug would have been potentially fatal given the large branches he used as supports. I sat up, glanced to my feet, and saw a whip like appendage wrapped around them. It tugged again and my back slammed right back into the ground with jarring force.

More of these bright red, whip-like appendages sprouted from the pit. The stayed there, five of them waving through the air as if charmed by some unheard tune before they stiffened suddenly. The whips slowly turned metallic black in color and large scythe-like blades exploded through the upper backside and top of the appendages simultaneously. The large blades glinted dangerously in the moonlight, looking as if they could through light itself.

The appendages sprung into action almost too fast for me to track and struck the ground with tremendous force around the pit Naruto had dug. There they stayed, in the craters formed by their explosive motion, blades deeply lodged into the earth.

I snapped out of my stupor and channeled chakra to my legs, encasing them in bright flames that force the whip-like appendage that took hold of my ankles to recoil away. I shuffled to me feet and searched for Kijiro, I may not have liked the man whatsoever but he was still a comrade. My eyes found him soon enough and narrowed at the sight. More of those wry appendages had slinked there way towards him. He was nearly covered from head to toe by the alien limbs. These limbs were different from the others, which were ether completely metallic black or completely this organic red. These appendages were thicker, had a more muscular appearance, and were spiked thoroughly. The appendages were mainly the metallic black but were striped in a spiraling fashion by a pulsating angry red organic material.

I could only watch on in horror as the appendages tore Kijiro in two in a gruesome display of gore and power. The monstrous appendages were pulled towards me at fast speeds and it was only my quick thinking that I jumped to a nearby branch and avoided being slammed by the limbs. I took a deep breath and channeled chakra to nearly every inch of my skin, setting me aflame. It was only the special fireproof fibers in my clothing and armor that kept me in full gear.

I knew my best bet would be to escape and return with backup. To alarm the Hokage… However, the more I thought on the matter the more I was compelled to stay. I knew the Hokage better than most people in the village and as much as it pains me to admit it; he was not to be trusted.

Therefore, I stayed and I watched as Naruto's form was pulled up and out of his self-made pit by the black whip like limbs that were attached to his black and anchored into the ground. I watched in grim satisfaction as Kijiro, one of the Hokage's undercover _ROOT _ANBU 'recruiters' was absorbed in a most sickly manner into Naruto. I smirked as I felt his chakra levels jump up afterwards and had to resist grinning as Naruto's form warped and took on Kijiro's. Soon after the appendages, sprouting from Naruto's body slinked back into him and his form reverted to normal. His body dropped to the earth below and stayed there.

Despite myself, I let a dark chuckle escape my throat. I now had the catalyst for my revenge on the aged Kage… Naruto… how… ironic.

* * *

Konoha General Hospital - Second Floor

* * *

In the sterile halls of Konoha's general hospital, two figures walked through the lone halls at a moderate pace. The two men were engaged in a hushed conversation as they made their way through the hospital to their destination. The taller figure was an elderly man with a dark complexion, hair grayed and eyes sharp as a knife as they looked over every detail that passed by. This man wore white robes with red trim, clothing signifying him as Sarutobi Hiruzen, the Sandaime Hokage. Besides him was another older man nearly covered head to toe in bandages. He held a gnarled walking stick in his hand as he walked at a pace his appeal would not suggest. This man is Shimura Danzo, head elder and advisor to the current Kage of Konoha.

Danzo's face was set into a frown as he walked alongside his life long rival. Things had not gone as he expected in the forest. He expected his ROOT recruiter to find the boy alongside the ex-ANBU Iruka. Instead, his agent was now dead, his body supposedly incinerated by the Kyuubi's volatile chakra. Iruka was still alive and was perfectly fine. He reported that only through his Dakajigan's ability to envelop its user in flames that he survived. It was all suspect to Danzo's intelligent mind.

However, there was nothing he could do about the matter, not even Hiruzen could refute Iruka's claims. His Dakajigan was a relatively new Kekkei Genkai and not much was known about it. Only Iruka's father, Masaki Umino, knew the most of the bloodline and he was dead, by the machinations of the Kage next to him.

Danzo pondered on the matter as he walked along side the Kage. The man was a shadow of his former self. Letting rage and despair overwhelm him. He had attempted many times to console his friend over the years but nothing could crack the shell that now calls itself Hiruzen.

Danzo could almost laugh at the irony. He was supposed to be the darkness that lied in the shadow of the great tree that was Konoha. He was to be the hatred that lingered beneath the surface. Now, Danzo found it hard to do the things he must for the village, he found it hard to hate. A role that the aged Sarutobi now gladly filled. For his heart was blackened with hate and rage. Ironic indeed that light and darkness found their roles switched.

"Danzo-kun," Came the voice of Hiruzen as he addressed his companion.

"Yes, Hokage-sama?" Danzo said respectively.

"What are your thoughts on the matter involving our young Jinchuruki?" He asked.

Danzo's eyes widened briefly as he contemplated his answer. Years ago he would have insisted that the brat be made into a heartless machine, meant only for the death and destruction of Konoha's enemies. Now he was not so sure.

"Hmm… I believe it would be best if we had Jiraiya return to the village to ensure the seal is intact." Danzo replied after some time.

"I see, I was thinking along the same Danzo-kun. We cannot afford to have this tool broken after all." Hiruzen said with a smirk.

Danzo managed to conceal his scowl from the Kage whose word continued to disgust the man.

Soon enough the two came to a stop in front of a door labeled 278. Hiruzen turned to address his advisor.

"Danzo-kun, enact protocol 5-B and insure that Jiraiya doesn't learn the truth during his short visit." The Kage ordered.

"… It will be done Hokage-sama." Danzo said whilst bowing towards the man. He turned on his heels and disappeared down the corridor.

After Hiruzen was sure his companion was gone he opened the door and walked into the room he was standing in front of.

"Danzo you fool…" He muttered softly as he approached the blond-haired boy laying in a medical bed before him. He took notice of the subtle changes in the boys physic. His hair was longer and now stopped just short of his shoulders, the scars on his face that resembled whisker marks were lighter and less refined, and he was slightly taller. His skin was a more healthy color and his body had much more mass to it.

Sarutobi Hiruzen frowned at these observations. '_It seems the Kyuubi has reversed the damage done to his body… this does not bode well for my plans._' The old man thought as he ran through several hand seals ending in an unorthodox tiger seal. His hands were enveloped in purple flames that soon turned blue.

'_I'll have to revert his body's physical state once more… hmhmhmm I'll enjoy this. _' The Hokage thought darkly before he placed his hands on Naruto's chest.

"Seinen no Mizo!" He whispered harshly as he completed the technique. The effects were instantaneous, in a matter of seconds Naruto's skin paled and his hair shortened. His body loss mass and his height reduced. His face reverted back to its earlier state.

Hiruzen's body experienced change as well, his skin lightened and the wrinkles marring his face softened, his hair darkened slightly and his back straitened. By all appearances, the Sandaime had just drained a portion of Naruto's life away.

'_There, that should keep you from developing any further for a couple of months and when you do, I'll just drain you again. Hmhmhmhmm I should thank you Kyuubi… by the end of his academy days I'll be back to my prime. Hmhmhmhmm_'

The old man was brought out of his thoughts when the door behind opened and closed. He turned to face the person that he'd been expecting.

"Ah, just on time Viper, as usual were having a visit from Jiraiya in a few scant hours. You'll need to disguise him once more."

"More of your dirty work old man…" Came the muffled voice of the hooded figure. Viper was of average height and fully clothed in baggy dark robes that revealed nothing of the figures gender. Viper's voice was masked and distorted by a purple mask with a coiling viper etched into the three inch thick metal.

"Now, now Viper, you know I am not as old as I used to be years before."

"Yes… a creation of desperation and fear old man…"

"And you know better than to insult your betters _Viper._"

"_Tsk_, whatever, your still an old man."

Hiruzen growled lowly as he slid to the side, allowing Viper to approach Naruto as he lay unconscious.

"You drained him again."

"…"

"Why are you doing this to him? He should be turning 13 this year."

"…My reason are my _own_, Viper."

"Your reasons will kill him!"

"He has the Kyuubi in him, he'll heal like he always does."

"…"

"…"

Silence reigned over the two as they stared at each other, neither willing to concede to the other in this test of wills. Finally, after several minutes Viper broke the silence.

"This is the last time Hiruzen." She spoke softly, knowing he would hear her.

"I will not need your _services_ again…"

"No! This is the last time you drain his life force! He's 13 with the physique of an seven year-old child!"

"Hmhmhm, and how do _you_ suppose you'll stop _me_? I am no longer frail and old Viper."

"…"

"I thought so… Do it. Now."

* * *

Mercer

* * *

I asked myself countless times why I did it. I could never find the answer. It didn't matter how deep I dug or how hard I tried to remember. The answer would always elude me. Even to this day, 5000 years later, I still was unaware of the only truth that mattered. The final truth about myself.

So here I am, asking the same question once more.

_Why did I do it? Why did I do this to myself? _

….

And again, as I suspected it would, the truth eluded me.

But maybe… this was the reason for it, meeting this boy… I don't care in any case. For now my existence will come to an end, and I couldn't be more content than this.

It all rests on this boys shoulders, the fate of the world. As for myself… I have a deranged mother to find in the afterlife…

* * *

The Next Day - Hokage's Office

* * *

"So what has the boy gotten himself into this time, sensei?"

Jiraiya, the tall, white-haired Spy-master/Sage spoke to his former sensei from the plush chair directly across from the Kage's own chair with an antiquated mahogany desk cluttered with paper work in between the two.

"Ah, that I do not know, Jiraiya-kun. However the seal may be disturbed, check on it will you?"

"Well I'll get right on that then, sensei." Jiraiya stated to his sensei before starting to stand.

"Jiraiya, I do hope you reconsider my offer to stay in the village this time around" Sarutobi asked with a small but serious smile.

Jiraiya stiffened for a fraction of a second before he sighed and turned to face his teacher again.

"Sensei… you know that I can't…" He started. "Ever since Minato and Kushina died… I just cant bear to be in this village. Maybe if Naruto was still alive I'd have stayed but… he didn't make it either…"

"Jiraiya…"

"I'm sorry sensei, truly… I'll send you a progress report on Akatsuki and Orochimaru in a months time, " At that Jiraiya's face turned from remorseful to serious almost instantly. He wasn't a legendary ninja without reason Sarutobi mused.

"He's planning something big sensei, probably an invasion from the looks of the increased activity I've been seeing." Jiraiya informed.

"Then let him come, The Will of Fire shall prevail." Sarutobi said with conviction.

"Yeah, it will… I'll go and take a look at Yori, then." Jiraiya said somberly

* * *

That's it, sorry for the wait and the shortness, been dealing with a lot of things so enjoy and be sure to review.

Next chapter: Revelations


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